SMTL ID : 9whe.1

A novel, covalent and highly synthetically accessible SARS-CoV-2 Mpro chloroacetamide inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x 01: (2~{R})-~{N}-[4,4-bis(fluoranyl)cyclohexyl]-2-[ethanoyl-[4-(1,2-thiazol-5-yl)phenyl]amino]-2-pyrazin-2-yl-ethanamide

01.1: 17 residues within 4Å: Chain A: H.41, C.44, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, D.187, R.188 Ligands: EDO.15 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.142, A:G.143, A:S.144, A:C.145 Water bridges: A:E.166 pi-Stacking: A:H.41

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 3 residues within 4Å: Chain A: R.40, N.84, C.85 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.40, A:N.84, A:G.179, A:G.179 Salt bridges: A:R.40

13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: V.35, H.80, S.81, K.88, K.90 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.79, A:H.80 EDO.4: 5 residues within 4Å: Chain A: E.166, L.167, P.168, Q.189 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.167, A:Q.189 EDO.5: 5 residues within 4Å: Chain A: G.215, D.216, R.217, W.218, R.279 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.216, A:R.217, A:R.279 Water bridges: A:R.217 EDO.6: 3 residues within 4Å: Chain A: Y.101, K.102, F.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.103, A:F.103 EDO.7: 1 residues within 4Å: Chain A: G.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.283 EDO.8: 6 residues within 4Å: Chain A: E.14, G.15, M.17, A.70, G.71, K.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.70 Water bridges: A:G.71 EDO.9: 4 residues within 4Å: Chain A: T.199, Y.239, L.287 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.239, A:L.287, A:L.287 EDO.10: 5 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, R.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.127, A:R.298, A:R.298 Water bridges: A:M.6 EDO.11: 3 residues within 4Å: Chain A: T.243, Q.244, D.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.244, A:D.245, A:D.245 EDO.12: 6 residues within 4Å: Chain A: Y.37, Q.83, K.88, F.103, L.177, E.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.177 Water bridges: A:E.178 EDO.13: 6 residues within 4Å: Chain A: R.131, L.287, E.288, D.289 Ligands: EDO.9, EDO.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.131, A:R.131, A:L.287, A:D.289 Water bridges: A:R.131 EDO.14: 7 residues within 4Å: Chain A: R.131, D.197, T.198, T.199, N.238, D.289 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.131, A:D.197, A:N.238 Water bridges: A:T.199 EDO.15: 6 residues within 4Å: Chain A: M.49, M.165, E.166, Q.189 Ligands: 01.1, EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.166, A:Q.189 Water bridges: A:E.166, A:Q.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zagribelnyy, B. et al., A novel, covalent and highly synthetically accessible SARS-CoV-2 Mpro chloroacetamide inhibitor. To Be Published

Release Date

2025-09-17

Peptides

3C-like proteinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3C-like proteinase

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